GEMMA_gwas_noncategorical

library(tidyr)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(ggplot2)
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

library(manhattanly)

## See example usage at http://sahirbhatnagar.com/manhattanly/

assoc_logistic <- read.table(file="/Users/vicegill/Documents/gemma_output.assoc.txt",header=TRUE)
assoc_logistic_filter <- assoc_logistic %>%
                      dplyr::filter(assoc_logistic$p_wald < 0.005)
assoc_logistic_filter$chr =as.numeric(assoc_logistic_filter$chr)
assoc_logistic_filter <- assoc_logistic_filter %>% filter(!is.na(chr))
manhattan_obj <- manhattanr(assoc_logistic_filter,chr="chr",bp="ps",p="p_wald")
manhattanly(manhattan_obj)